What I'm doing, thinking about, watching, and listening to right nowby Megan Sperry​​

Lauren Graham's new book, Talking as Fast as I Can // lauren-online.net

thinking about: graduate student unions

​Graduate student unions (or attempts to form them) are making headlines this month. Although many state universities formed graduate student unions in the 1990s (governed by state labor laws), private universities were previously restricted from forming unions by the National Labor Relations Board (NLRB). This restriction was reversed in August 2016 when the NLRB decided that graduate students are classified as ‘statutory employees’. This group includes graduate student teaching assistants and research assistants who are paid by the university. The purpose of such unions is to bargain for wages, benefits, and policies. For example, the University of California graduate student union has taken on issues like class size control for teaching assistants, increased financial assistance for undocumented students, and the installation of gender-neutral bathrooms. So, who is getting involved and where are they at? Here are some examples:

University of Pennsylvania: The group Graduate Employees Together (GET-UP) is leading the effort to form a union. They are hoping to hold a vote by May 2017.

Harvard: Students voted on unionization in November; some ballots remain under challenge because Harvard and the union disagree over which jobs qualify as teaching or research.

Duke: Voted in February, with 691 students against the union and 398 in favor. However, ballots were identified from individuals not enrolled as students.

Yale:In February, the Math, Sociology, History, History of Art, English and Geology and Geophysics departments voted to unionize. The Physics Department voted against unionization.

Columbia:Voted to unionize, with 1,602 in favor and 623 against. However, Columbia University is claiming that the election was invalid since voters did not have to show identification

While I support the right to unionize, I also see the challenges to unionizing student-workers. (Stay tuned for a future article where I outline the benefits and concerns!) I am interested to see how unionization will pan out in this unique situation. Also, keep an eye on the composition of the NLRB under the Trump administration. The August 2016 ruling could be overturned, halting all efforts.

Private universities are voting to unionize // via Brown Daily Herald

doing: taking in the art of neuroscience

​You might remember the BPC article from 2015 that featured Gregg Dunn and Brian Edwards’ work. Well, last year they finished a huge piece, Self Reflection, which now lives in the Franklin Institute. I had the chance to see it this week and it was amazing. The piece is a microetching of the human brain with gold plating and 144 LED lights. I was most impressed by the deep scientific underpinnings of the artwork. The etching technique is capable of yielding animations that depict true brain activity, based on simulations that the artists studied. (FYI: These guys are also scientists!) Dunn’s website features an in-depth explanation of the process used to create Self Reflection, including studying neuron microscopy, reconstructing diffusion spectrum imaging, and mathematically simulating neuron activity, including:

Using these data, we then used algorithmic and mathematical simulations to chaotically link up the center points of neurons with the end points of axons and to infuse causality into the connectivity, the most complex part of the project. As microetchings are animated, these connections have timings associated with them and influence connections later made within complex neural circuits. We could control action potential speed, bursting vs. tonic behavior, axon diameter, degree of randomness in connectivity, etc.

A short video I recorded of Self Reflection at the Franklin Institute.

reading: Talking as Fast as I Can

After a winter of historical fiction (I just finished a dense novel by Philippa Gregory), it was time for something a little lighter. Right now, I am reading Talking as Fast as I Can:From Gilmore Girls to Gilmore Girls (and Everything in Between), by Lauren Graham. Yes--that Lauren Graham of Gilmore Girls fame. Her writing is just as frenetic as the speech patterns of her alter-ego Lorelai Gilmore. Each chapter is a distinct essay, with topics ranging from the perception of age in Hollywood to the future stars that guested on Gilmore (remember John Hamm in season 3?). Graham wrote the book, in part, while filming the Gilmore reboot in spring 2016, so I am particularly excited to read those essays.​

watching: Wonder Woman

via wonderwomanfilm.com

I am certainly not a superhero/comic book buff, but the new Wonder Woman trailer caught my eye recently and sent me into a black hole of research. Who is Wonder Woman? Well, she turned 75 this year (!) and had quite the range of looks over the years. For those of you less familiar, she was trained in the Amazon and has superior hunting abilities, combat skills, and strength. She also speaks many languages and has deep scientific knowledge, relying on a large collection of advanced technology. Despite her original launch during WWII, she became a feminist icon after she was promoted by Gloria Steinem on the first cover of Ms magazine in 1972. I'm hoping the Summer 2017 version of Wonder Woman is just as amazing.

And a little something funny...

This post is brought to you by Benchling. Thank you for supporting the sponsors of BPC!

I go through one of these puppies in less than 6 months.

​by Heidi Norton​Ever since my sophomore year of college when I got my very own hard-bound, very official looking lab notebook, I’ve enjoyed the process of keeping a lab notebook (maybe a little too much...). Print-outs of every gel I ran would be lovingly taped into the pages; so would protocols with dozens and dozens of steps. I would draw schematics of my experiments, draw big smiley faces on days my experiments worked, and sad emojis when things failed. Keeping up this methodical notebook took time. No joke, I must have spent at least two hours a week cutting and taping. And oh man, can I go through a paper lab notebook quickly!​So far in my research career, I’ve spent significant time in 5 research labs (oddly enough, four of these begin in a C: Cockett, Cochran, Chen, and Cremins!) and have had to leave my lovely lab notebooks behind. I kept adequate digital copies of protocols from all the labs I’ve been in, but if I ever want to take a walk down memory lane and look at gel images of yester-year, I’m out of luck. Even more important than science nostalgia, if I ever want to find a protocol that I used a few years ago to replicate an experiment, I have to comb through pages and pages in my dozens of paper notebooks.

I’ve been interested in the concept of a digital lab notebook for a while exactly because of this issue – I want to be able to access my lab notebook from my current lab and previous labs from anywhere and easily find a lab notebook entry or protocol in seconds. I’d known fellow graduate students who have used digital note-taking applications as a lab notebook and I had toyed with the idea a few times. Ultimately, I was concerned about how easily some notes could be deleted and how difficult it would be for other lab members to access my lab notebook.

I first heard about Benchling at a happy hour that they sponsored for grad students in my department. They passed out free t-shirts with their cool logos and made a pitch for their new concept for a digital lab notebook that streamlines the scientific collaboration process through easy search-ability and seamless integration with cloning tools. As soon as I got back to my lab after the happy hour, I set up an account and was instantly excited. (I know this might sound too enthusiastic, especially because this is a sponsored post – but I’m not exaggerating here. It was exactly what I was looking for!). I noticed that digital back-ups of my notebook entries were automatically saved regularly and that I could easily share my whole notebook or individual entries with my labmates.

Benchling offers a digital lab notebook that makes scientific collaboration so much easier!

The first thing that excited me about Benchling is its calendar lab notebook view. I can create a multi-day lab notebook entry for a given project, but also have another multi-day lab notebook entry spanning the same days for a different project. This works great for me when I have multiple projects that I work on in a given week, the details of which easily become disorganized in a paper lab notebook. I can easily click on my calendar to view which experiments I completed that day, but can also click through consecutive entries for a given project. And, I was excited to find the feature that I can export my lab notebook entries in chronological order spanning all projects and print them into a hard copy lab notebook to have as a back-up.

The calendar view is one of my favorite features of Benchling. Projects are color-coded and entries can span multiple days.

Once I realized how much utility Benchling could have in my research, I started telling my labmates about it. We loved how easily we could share protocols and view each others’ plasmid designs. Soon, enough of us were using it that we did a lab-wide trial run.​Around the same time, I started transitioning from entirely wet-lab (experiments at the bench) to a substantial amount of dry-lab (writing code to analyze and model our data). I’m finding that Benchling is a great way for me to keep track of the directory I’m working from for a given task, what the goals/problems I’m trying to solve are, and relevant snippets of code. This would be literally impossible with a paper lab notebook (ok, not totally impossible, but so so tedious).​

Benchling lab notebook entries are easily searchable and integrate with their intuitive cloning tools. You can even add tables with calculations, timers, and checklists. Click the image to try it!

​Another huge upside for me is that it is 1,000x easier to find a labmate’s protocol by clicking on their Benchling notebook and searching ‘Neural Stem Cell plate coating’ than by searching for 20 minutes for the hard copy lab notebook and spending another 20 minutes flipping through the pages to maybe find the right entry with difficult-to-read handwriting.​

You can link protocols to your Benchling notebook entries. I especially like the ability to track the amount of time it takes to complete a step with timers integrated directly into the protocol. Click the image to try it!

​In short, I love the organizational capabilities of Benchling because it helps me keep track of multiple projects in a coherent manner, allows me to access my lab notebook from anywhere, helps me easily search through my colleagues’ lab notebook entries (without the risk of me modifying their entries), and offers a solution for keeping a record of computational lab work.

Stay tuned for Benchling’s re-design that has some awesome new organizational tools. One of the things that I’m interested in is ability to perform sample inventory, which looks like it will have awesome utility especially for tracking cell lines.​In case you needed any additional convincing, Benchling’s cloning tools are so cool that they deserve their own post, but I’ll give you a teaser. In the 5 minutes between writing paragraphs as I was thinking about what I wanted to say, I downloaded the gene in the specific assembly of the murine genome I want to edit, designed guide RNAs for the CRISPR nickase system to edit my locus of interest, selected the guide pair with the highest on-target score and lowest off-target score that fit my overhang criteria, and assembled the guide RNAs into my lentiviral puro-selection plasmid of interest – all without leaving the Benchling interface.

Benchling’s plasmid viewer allows you to design all of your cloning experiments in situ before you even touch a pipet. Click the image to try it!

If you’ve ever wondered about using a digital notebook, or if you never even knew you needed a digital lab notebook in your life but now you’re curious, check out Benchling here!​